River buffalo, Bubalus bubalis is a large bovine species frequently used livestock in southern Asia. It is believed that the river buffalo was domesticated from Bubalus arnee, the wild buffalo of mainland Asia, a few thousand years ago, probably during the period of Indus Valley civilization. However, the domestication history of the river buffalo has been the subject of debate for many decades mainly due to the lack of clear archeological evidence and the divisive conclusions of the genetic studies. Therefore, in order to understand the domestication history and genetic relationship among the various river buffalo populations, we analyzed 492-bp region of mitochondrial DNA control region sequences of 414 river buffalo sampled from India, Pakistan, Egypt, and Iran along with the available 403 swamp buffalo sequences. The phylogenetic analyses of our study along with the archaeological evidence suggest that the river buffalo was domesticated in an atypical manner involving continuous introgression of wild animals to the domestic stocks in Indian subcontinent prior to mature phase of Indus Valley civilization (2600–1900 BC). Specifically, our data exclude Mesopotamian region as the place of domestication of the river buffalo.

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